The continued creation of unique and ingenious genetic tools by many drosophilists over the past century has transformedDrosophilainto a powerful model organism for diverse topics in biomedical research. However, technical issues on efficiently regulating target gene expression remain to be fixed inDrosophila. To further promote our research, we have made a significant effort in developing novel genetic tools for the whole fly community in the past five years, including: (1) Developed and optimized a genome editing method inDrosophilabased on the CRISPR/Cas9 system, which has the characteristics of simplicity, high-efficiency and specificity (2) Successively developed two versions of CRISPR/dCas9 based transcriptional activation system inDrosophilathat can efficiently activate target gene. Using the later flySAM transcriptional activation system, genome-wide transgenic activation fly resources were constructing, which is the first transgenic overexpression library around the world. (3) Developed the next generation transgenic RNAi technique inDrosophila, which exhibited higher efficiency and lower toxicity, thus decreased the false negative and false positive results respectively. Importantly, for the first time we can target multiple genes with one construction using this system.These novel genetic tools and corresponding transgenic fly resources are made in Tsinghua Fly Center and available for the entire fly community (https://thfc.zzbd.org), and will have broad impact on the research efforts in understanding development and diseases.

Stem cells can self-renew and differentiate into diverse cell types to maintain tissue homeostasis, and abnormal behaviors of stem cells are the leading cause of developmental disorders and diseases such as cancer and infertility. Equipped with above genetic tools, we successfully investigated the coordination between epigenetic factors and signaling pathways.

(#corresponding author)

1.J Sun, X Wang, R Xu, D Mao, D Shen, X Wang, Y Qiu, Y Han, P Peng, X Kang, R Zhu, Y Jia, X Lu, YLi, J Yu, Y Wang, L Liu, Z Chang, J Ji, Z Wang, QLiu, S Li^#, F Sun^#,JQ Ni^#，HP1c regulatesdevelopment and gut homeostasis by suppressing Notch signaling through Su(H)，EMBOReport，PMID: 33594776 DOI: 10.15252/embr.202051298

2.Y Gao; Y Mao; R.G Xu; R Zhu; M Zhang; J Sun; D Shen; P Peng; T Xie^#;J.Q Ni^#_，Defining Gene Networks Controlling the Maintenance and Function of the Differentiation Niche by an in vivo Systematic RNAi Screen,J Genet Genomics. Jan 20 2019. 46(1) 19-13

3. Qiao HH, Wang F, Xu RG, Sun J, Zhu R, Mao D, Ren X, Wang X, Jia Y, Peng P, Shen D, Liu LP, Chang Z, Wang G, Li S, Ji JY, Liu Q,Ni JQ^#An efficient and multiple target transgenic RNAi technique with low toxicity in Drosophila,NATURE COMMUNICATIONS, 2018 Oct 8;9(1):4160. doi: 10.1038/s41467-018-06537-y.

4. Zheng Y, Xue Y, Ren X, Liu M, Li X, Jia Y, Niu Y,Ni J.Q^#,Zhang Y^#, Ji JY^#. The Lysine Demethylase dKDM2 Is Non-essential for Viability, but Regulates Circadian Rhythms in Drosophila.Front Genet. 2018 Sep 4;9:354. doi: 10.3389/fgene.2018.00354.

5. Y Jia, R.G Xu, X Ren, B Ewen-Campen, R Rajakumar, J Zirin, D Yang-Zhou, R Zhu, F Wang, DMao, P Peng, H.H Qiao, X Wang, L.P Liu, B Xu, J.Y Ji, Q Liu, J Sun^#, N Perrimon^#,NiJ.Q^#, Next-generation CRISPR/Cas9 transcriptional activation in Drosophila using flySAM,Proc Natl Acad Sci USA. 2018 May 1;115(18):4719-4724. doi: 10.1073/pnas.1800677115.

6. Ewen-Campen, B., Yang-Zhou, D., Fernandes, V.R., Gonzalez, D.P., Liu, L.P., Tao, R., Ren, X., Sun, J., Hu, Y., Zirin, J., Mohr, S.E.,Ni J.Q^#, and Perrimon, N^#. Optimized strategy for in vivo Cas9-activation in Drosophila.Proc Natl Acad Sci USA. 2017 Aug 29;114(35):9409-9414. doi: 10.1073/pnas.1707635114.

7. Yang, Z., Sun, J., Hu, Y., Wang, F., Wang, X., Qiao, H.H., Xu, J., Mao, D., Ren, X., Pan, L.X., Xu, R.G., Xu, B.W., Zhang, Y., Li, H., Miao, W., Hu, Y., Chang, Z., Wang, D., Li, H., Chang, Z., Liu, L.P., Liu, Q.,Ni, J.Q^#. Histone H1 defect in escort cells triggers germline tumor in Drosophila ovary.Developmental biology. 2017 Apr 1;424(1):40-49. doi: 10.1016/j.ydbio.2017.02.012.

8. Lu T, Wang S, Gao Y, Mao Y, Yang Z, Liu L, Song X,Ni JQ^#,Xie T^#. COP9-Hedgehog Axis Regulates the Function of the Germline Stem Cell Progeny Differentiation Niche in the Drosophila Ovary,Development. 2015 Dec 15;142(24):4242-52. doi: 10.1242/dev.124768.

9. Sun J, Wei HM, Xu J, Chang JF, Yang Z, Ren X, Lv WW, Liu LP, Pan LX, Wang X, Qiao HH, Zhu B, Ji JY, Yan D, Xie T, Sun FL^#,Ni JQ^#. Histone H1-Mediated Epigenetic Regulation Controls Germline Stem Cell Self-Renewal by Modulating H4K16 Acetylation,Nature Communications. 2015 Nov 19;6:8856. doi: 10.1038/ncomms9856.

10. Pan L, Xie W, Li KL, Yang Z, Xu J, Zhang W, Liu LP, Ren X, He Z, Wu J, Sun J, Wei HM, Wang D, Xie W, Li W,Ni JQ^#, Sun FL^#. Heterochromatin remodeling by CDK12 contributes to learning in Drosophila,Proc Natl Acad Sci USA. 2015 Nov 10;112(45):13988-93. doi: 10.1073/pnas.1502943112.

11. Xu J, Ren X, Sun J, Wang X, Qiao HH, Xu BW, Liu LP,Ni JQ^#, A Toolkit of CRISPR-Based Genome Editing Systems in Drosophila,J Genet Genomics. 2015 Apr 20;42(4):141-9.

12. Ren X, Yang Z, Xu J, Sun J, Mao D, Hu Y, Yang SJ, Qiao HH, Wang X, Hu Q, Deng P, Liu LP, Ji JY, Li JB^#,Ni JQ^#, Enhanced specificity and efficiency of the CRISPR/Cas9 system with optimized sgRNA parameters in Drosophila.Cell Reports. 2014 Nov 6;9(3):1151-62.

13. Pan L, Wang S, Lu T, Weng C, Song X, Park JK, Sun J, Yang ZH, Yu J, Tang H, McKearin DM, Chamovitz DA,Ni JQ, Xie T^#. Protein competition switches the function of COP9 from self-renewal to differentiation.Nature. 2014 Oct 9;514(7521):233-6.

14. Ren X, Sun J, Housden BE, Hu Y, Roesel C, Lin S, Liu LP, Yang Z, Mao D, Sun L, Wu Q, Ji JY, Xi J, Mohr SE, Xu J^#, Perrimon N^#,Ni JQ^#. An optimized gene editing technology for Drosophila melanogaster using germline-specific Cas9,Proc Natl Acad Sci USA. 2013 Nov 19;110(47):19012-7.

15.Ni JQ, Zhou R, Czech B, Liu LP, Holderbaum L, Yang-Zhou D, Shim HS, Tao R, Handler D, Karpowicz P, Binari R, Booker M, Brennecke J, Perkins LA, Hannon GJ, Perrimon N^#. A genome-scale shRNA resource for transgenic RNAi in Drosophila .Nature Methods. 2011 May;8(5):405-7.

16.Ni JQ, Liu LP, Binari R, Hardy R, Shim HS, Cavallaro A, Booker M, Pfeiffer BD, Markstein M, Wang H, Villalta C, Laverty TR, Perkins LA, Perrimon N^#. A Drosophila Resource of transgenic RNAi lines for Neurogenetics. Genetics. 2009 Aug;182(4):1089-100.

17.Ni JQ, Markstein M, Binari R, Pfeiffer B, Liu LP, Villalta C, Booker M, Perkins L, Perrimon N^#. Vector and parameters for targeted transgenic RNA interference in Drosophila melanogaster.Nature Methods. 2008 January; 5(1): 49–51.

18.Ni JQ, Liu LP, Hess D, Rietdorf J, Sun FL^#. Drosophila ribosomal proteins are associated with chromatin through histone H1 and suppress global transcription.Genes Development. 2006 Jul 15;20(14):1959-73.

19. Liu LP*,Ni JQ*, Shi YD, Oakeley EJ, Sun FL^#. Sex-specific role of Drosophila melanogaster HP1 in regulating chromatin structure and gene transcription.Nature Genetics. 2005 Dec;37(12):1361-6.(*co-first author)